UBP8 ubiquitin-specific protease UBP8 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: UBP8
Official Full Name: ubiquitin-specific protease UBP8
Primary source: SGD:S000004836
Locus tag: YMR223W
See related: AllianceGenome:SGD:S000004836; FungiDB:YMR223W; VEuPathDB:YMR223W
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Summary: Enables cysteine-type deubiquitinase activity and molecular adaptor activity. Involved in RNA splicing. Part of DUBm complex; SAGA complex; and SLIK (SAGA-like) complex. Used to study glioblastoma. Human ortholog(s) of this gene implicated in non-syndromic X-linked intellectual disability 105. Orthologous to several human genes including USP27X (ubiquitin specific peptidase 27 X-linked). [provided by Alliance of Genome Resources, Oct 2024]
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Genomic context

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See UBP8 in Genome Data Viewer

Location:: chromosome: XIII

Exon count:: 1

Sequence:: Chromosome: XIII; NC_001145.3 (716715..718130)

Chromosome XIII - NC_001145.3 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001145.3

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Gcn5p and Ubp8p Affect Protein Ubiquitylation and Cell Proliferation by Altering the Fermentative/Respiratory Flux Balance in Saccharomyces cerevisiae.
Title: Gcn5p and Ubp8p Affect Protein Ubiquitylation and Cell Proliferation by Altering the Fermentative/Respiratory Flux Balance in Saccharomyces cerevisiae.
SAGA-CORE subunit Spt7 is required for correct Ubp8 localization, chromatin association and deubiquitinase activity.
Title: SAGA-CORE subunit Spt7 is required for correct Ubp8 localization, chromatin association and deubiquitinase activity.
We show here that mutating the active site cysteine of human USP4 and yeast Ubp8 to alanine increases the affinity of the DUB for mono- or diubiquitin by 10-150-fold.
Title: Active site alanine mutations convert deubiquitinases into high-affinity ubiquitin-binding proteins.
an unexpected role for Sgf11 in compensating for the absence of structural features that maintain the active conformation of Ubp8.
Title: A role for intersubunit interactions in maintaining SAGA deubiquitinating module structure and activity.
Ubp8 can deubiquitinate Snf1, a highly conserved AMP-activated serine/threonine protein kinase that serves as an energy sensor in the cell.
Title: Ubp8 and SAGA regulate Snf1 AMP kinase activity.
study reports the 1.90 angstrom resolution crystal structure of the deubiquitinating module (DUBm)- which contains Ubp8 bound to Sgf11, Sus1 and Sgf73- bound to ubiquitin aldehyde, as well as the 2.45 angstrom resolution structure of the uncomplexed DUBm
Title: Structural insights into the assembly and function of the SAGA deubiquitinating module.
Structural and functional analyses reveal a central role of Sgf11 and Sgf73 in activating Ubp8 for deubiquitinating histone H2B and demonstrate how a DUB can be allosterically regulated by its nonsubstrate partners.
Title: Structural basis for assembly and activation of the heterotetrameric SAGA histone H2B deubiquitinase module.
Ubp8 is a part of the SAGA complex and its deubiquitylation activity requires Ubp8's association with SAGA.
Title: The deubiquitylation activity of Ubp8 is dependent upon Sgf11 and its association with the SAGA complex.
Thus, the Sus1-Sgf11-Ubp8 module could work at the junction between SAGA-dependent transcription and nuclear mRNA export.
Title: The mRNA export factor Sus1 is involved in Spt/Ada/Gcn5 acetyltransferase-mediated H2B deubiquitinylation through its interaction with Ubp8 and Sgf11.
mechanism by which H2B ubiquitylation acts as a barrier to Ctk1 association with active genes, while subsequent deubiquitylation by Ubp8 triggers Ctk1 recruitment at the appropriate point in activation
Title: H2B ubiquitylation acts as a barrier to Ctk1 nucleosomal recruitment prior to removal by Ubp8 within a SAGA-related complex.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Pathways from PubChem

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

Gene Ontology Provided by SGD

Function	Evidence Code	Pubs
enables cysteine-type deubiquitinase activity	IEA Inferred from Electronic Annotation more info
enables cysteine-type deubiquitinase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables cysteine-type peptidase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables molecular adaptor activity	IDA Inferred from Direct Assay more info	PubMed
enables molecular adaptor activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	RCA inferred from Reviewed Computational Analysis more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA splicing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein deubiquitination	IEA Inferred from Electronic Annotation more info
involved_in proteolysis	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of DUBm complex	IDA Inferred from Direct Assay more info	PubMed
part_of SAGA complex	IDA Inferred from Direct Assay more info	PubMed
part_of SLIK (SAGA-like) complex	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: ubiquitin-specific protease UBP8

NP_013950.1

EC 3.4.19.12

Ubiquitin-specific protease component of the SAGA acetylation complex; required for SAGA (Spt-Ada-Gcn5-Acetyltransferase)-mediated deubiquitination of histone H2B

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_001145.3 Reference assembly

Range

716715..718130

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001182730.1 → NP_013950.1 TPA: ubiquitin-specific protease UBP8 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_013950.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D6W048, P50102

UniProtKB/TrEMBL

A6ZMT5, B3LMB1, C7GRC8, C8ZF87, G2WKT0, N1P0J5

Conserved Domains (2) summary

cd02660
Location:138 → 466

Peptidase_C19D; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

pfam02148
Location:46 → 108

zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein